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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatttgccatattcatcaagactcttatggattcataactatttcatgataattagctccttgattgcatgttgatttttacggtaaagctatgt...

Basic information

species Glycine max
transcript GLYMA18G02970.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: AT5G22440.1 (Arabidopsis thaliana), 5'ss of exon 3
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatttgccatattcatcaagactcttatggattcataactatttcatgataat-tagctccttgattgcatgttgatttttacggtaaagctatgt
 || ||||||||| | || || || ||||| ||  |||| ||| | ||| | || |||||||| |||||||||||||||||||| ||||| || ||||||||     |||  |    |  ||     | | |     | || | || | | |  || | |||  |  | | |    |||| |||     |           
TCAAAAGGACAAGAGATTTAGCGGTTCTGTGAAATTGCCTCACGTTCCTAGGCCAAAGATGAAGATTTGCATGCTTGGTGATGCCCAGCACGTCGAAGAGgttcacttttttccgccttttc----ttttgaaaatgttatgattagtacttagtagtatagtactataacttgcggttggtttacttag-----------

upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: AT2G27530.1 (Arabidopsis thaliana), 5'ss of exon 3
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctct--atttgccatattcatcaagactcttatggattcataactatttcatgataattagctccttgattgcatgttgatttttacggtaaagctatgt
||| ||||| |||||||||||||| ||||| ||||| || || || |||||||| || ||||| || || |||||||| ||||||||||||||||| |||||   |  | |  | ||| |  |   |  |||| |    |   || |  |   ||| |   ||     || ||| |||||  |||| |  |           
ACAAAAGGATAAGCGTTTCAGTGGATCTGTGAAGCTCCCACATATTCCTCGCCCAAAAATGAAGATCTGTATGCTTGGAGATGCTCAGCATGTTGAGGAGgtgattgaaatctctatactttttgtgtatcttgtttggtttgaattggtgattgacacaaag-----tgtttg-atgtttgttttgatag-----------

upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G08360.1 (Arabidopsis thaliana), 5'ss of exon 3
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtc-tctat-ttgccatattcatcaagactcttatggattcataactatttcatgataattagctccttgattgcatgttgatttttacggtaaagctatgt
 || |||||||||||||||||||| ||||||||| | || || ||||| || || || ||||| || |||||||| || ||||| |||||||||||||||||  | ||| ||  |||    ||  |   | || ||   |  |   | | | ||| |  |  |||| ||  |    || ||  | |    ||     |   |
TCAAAAGGACAAGCGTTTCAGTGGATCTGTCAAGTTACCACATATCCCCCGTCCTAAAATGAAGATCTGCATGCTCGGAGATGCCCAGCATGTTGAAGAGgtgatatatcttttcatggaaattgatcattttgtgctctgtttcttgtataatggttttgtgctcatt--tcatttggtggctctattagtttcatttgat

upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: Vv06s0080g00400.t01 (Vitis vinifera), 5'ss of exon 5
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatttgccatattcatcaagactcttatggattcataactatttcatgataattagc-tccttgattgcatgttgatttttacggtaaagctatgt----
 ||||||||||||||||||||||| ||||| ||| ||||||||||||||||||||||||||||  | |||||||||||||||||||| || || ||||||||   | |   |||    | |     |  | ||||    | ||  | |  | || || |  | |   | |||| |   | ||||||    ||    | |||    
CCAGAAGGACAAGCGTTTCAGTGGTTCTGTGAAGTTGCCCCACATCCCTCGCCCCAAGATGAAGGTCTGCATGCTTGGTGATGCTCAACACGTGGAAGAGgtaattgtgctcca----cttggctgcattaatggcaataaaagaagtgaaagacaagtgtcattgctaattgaagaat-atttttcaactatttttttgtttaa

upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S40_297V6.1 (Physcomitrella patens), 5'ss of exon 2
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatttgccatattcatcaagactcttatggattcataactatttcatgataattagctccttgattgcatgttgatttttacggtaaagct-atgt--------
 ||||| ||||| |||||||| |||||||| |||||||| ||||| ||||| || ||||||| | | ||||||||||| ||||||||||| || || ||||||  |||| || | |||    || | | || ||  ||||||  | ||||||  | |  |    |||||||      | |||| |     || | | || |        
CCAGAAAGACAAACGTTTCAGCGGCTCTGTGAAGCTGCCACACATTCCTCGTCCTAAGATGAGAGTGTGCATGCTTGGAGATGCTCAGCACGTCGAGGAGgtca-tattcgc-acattgg--aataatttt-tgccttcatatttgtttcatttttag-attatcttgattaatgtctcatttcttaaccaacgttcatctgacaatag

upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S427_1V6.1 (Physcomitrella patens), 5'ss of exon 2
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgt----------------ctctatttgccatattcatcaagactcttatggattcat--aactatttcatgataattagctcc----ttgattgcatgttgatttttacggtaaagctatgt-----------------------------------------------------------------------
 ||||| |||||||||||||||||||| || ||||| |||||||| ||||| || |||||||  ||||| |||||||| ||||| || ||| ||||||||||                 |  |||     ||||  |  |   |   |   ||| |   ||  |||  |  ||  |  ||||      | ||  ||      ||| ||   |||| |||                                                                          
CCAGAAAGACAAGCGTTTCAGTGGCTCCGTGAAGCTTCCCCACATTCCTCGTCCTAAGATGAGGATTTGTATGCTTGGAGATGCCCAACATATTGAAGAGgtatgcttattctcaaattttgattctttctatttgttgatggtgccagaaattgaataaaacattgtagaattttctgctctgggtctcatctcactggcctttgtatattaaaactagaaattatcaccctttacttgataatggataattgctgatgtcgtgagtttcttttggtcgtaactcgtcacag

upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: PP1S18_121V6.1 (Physcomitrella patens), 5'ss of exon 2
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatt-tgccatattcatcaagactcttatggattcataactattt--catgata-atta-gctccttgattgcatgttgatt-tttacggtaaagctatgt-----
 ||||| ||||||||||||||||| || || |||||||| ||||| |||||||| ||||||    | |||||||| || ||||| ||||| ||||| ||||| | |  | |  |  |   |     || | | | ||     |  |  |   ||||  | |||| ||   |||||| | | ||  || ||  |   |    |  ||     
CCAGAAAGACAAGCGTTTCAGTGGTTCCGTGAAGCTGCCACACATTCCTCGCCCTAAGATGCGCGTGTGCATGCTCGGAGATGCCCAGCACGTTGAGGAGgtatttcctctaactcaactaatgccacccatgttgagaagcattttgtcagcatgccacattacgcaggttgattacctcttatttattcgccccattattgcgtaacag

upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ31249 (Selaginella moellendorffii), 5'ss of exon 2
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatttgccatattcatcaagactcttatggattcataactatttcatgataattagctccttgattgcatgttgatttttacggtaaagctatgt
 |||||||||||||||||||| ||||| || |||||||| |||||  | || |||||||||| | | |||||||| |||||||| |||||||| |  |||||    |||   |    ||       ||| | | | | |   | |   |||   |  |    | |||  |||||                          
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCGCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGCGAGgtaag-attgagcgccctc------tctcctttagttgccggattgaatcac--tggtccattgcttttttgcacag-----------------------

upper sequence: GLYMA18G02970.1 (Glycine max), 5'ss of exon 1
lower sequence: EFJ34353 (Selaginella moellendorffii), 5'ss of exon 2
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatttgccatattcatcaagactcttatggattcataactatttca-tgataattagctccttgattgcatgttgatttttacggtaaagctatgt
 |||||||||||||||||||| ||||| || |||||||| |||||  | || |||||||||| | | |||||||| |||||||| |||||||| |  |||||    |||   |    |      | ||| | | | | |   | |   ||| || |   | |||  ||  |||||                          
GCAGAAGGACAAGCGTTTCAGCGGCTCGGTGAAGCTGCCTCACATTGCCCGGCCCAAGATGAGAGTGTGCATGCTCGGTGATGCGCAGCATGTAGGGGAGgtaag-attgagcgccct------gtctccttttgttgccggattgaatcactggtccgttgcttttt--ttgcacag-----------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|298194279|gb|HO040927.1|HO040927
EST:     GCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAG                         GCGGAGAAGATAGGACTGGACTGGATGGATGTGGAAGCCCTGAAGAAG
genomic: GCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctattt ... ctatctgtagGCGGAGAAGATAGGACTGGACTGGATGGATGTGGAAGCCCTGAAGAAG
EST: gi|207823736|gb|GD797085.1|GD797085
EST:     CAAGATGAAAATTTTGTCATGCTTGGTGATGCTCAGCATGTTGAAGAG                         GCGGAGAAGATAGGACTGGACTGGATGGATGTGGAAGCCCTGAAGAAGCTA
genomic: CAAGATGAAAA-TTTG-CATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctattt ... ctatctgtagGCGGAGAAGATAGGACTGGACTGGATGGATGTGGAAGCCCTGAAGAAGCTA
EST: gi|14009228|gb|BG725832.1|BG725832
EST:     GCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAG                         GCGGAGAAGATAGGACTGGACTGGATGGATGTGGAAGCCCTGAAGAAGCTA
genomic: GCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctattt ... ctatctgtagGCGGAGAAGATAGGACTGGACTGGATGGATGTGGAAGCCCTGAAGAAGCTA
EST: gi|7234411|gb|AW569749.1|AW569749
EST:     GCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAG                         GCGGAGAAGATAGGACTGGACTGGATGGATGTGGAAGCCCTGAAGAAGCTA
genomic: GCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctattt ... ctatctgtagGCGGAGAAGATAGGACTGGACTGGATGGATGTGGAAGCCCTGAAGAAGCTA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGAAGGACAAGCGTTTCAGTGGCTCTGTCAAGCTGCCCCACATCCCTCGCCCCAAGATGAAAATTTGCATGCTTGGTGATGCTCAGCATGTTGAAGAGgtctctatttgccatattcatcaagactcttatggattcataactatttcatgataattagctccttgattgcatgttgatttttacggtaaagctatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA